FILTERBAM(1)

💅 filterBam — like, the manual page (FILTERBAM(1)) ✨

okay bestie, sit down, hydrate, and let me tell you about filterBam 🫶 it filters a BAM file so your AUGUSTUS tools can actually use it. glowy. iconic. let's go 🎀

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🌸 NAME 🌸

filterBam — filter BAM file for use with AUGUSTUS tools ✨

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🦋 SYNOPSIS 🦋

filterBam --in in.bam --out out.bam [options]

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💖 DESCRIPTION 💖

okay so here's the tea, and it is NOT optional: your input file must be sorted lexicographically by 'queryname'. no vibes-based sorting. lexicographic. periodt 👑

here's how you make that happen:

• Convert the file into SAM format, sort lexicographically by queryname and convert back again into BAM format. E.g.

export LC_ALL=C
samtools view -H file.bam > file_sorted.sam
samtools view file.bam | sort -k 1 >> file_sorted.sam
samtools view -bS file_sorted.sam > file_sorted.bam

(be aware: 'export LC_ALL=C' might be used because sort ignores characters like ':') 🙈

Also, please bear in mind that this will require converting your BAM file into SAM. no skipping that step, babes.

• samtools and bamtools provide facilities to do the sorting, but they are not guaranteed to work because of the problem mentioned above 😭 (the whole ':'-ignoring thing. yeah. that one.)
• In the case of samtools, the command to sort by 'queryname' is:

samtools sort -n -o file_sorted.bam file.bam

For more information check the man page included in samtools distribution. iykyk 📖

• bamtools can also sort bam files:

bamtools sort -byname -in file.bam -out file_sorted.bam

but only provides the option to do it by queryname. that's the whole menu, bestie 🍓

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✨ OPTIONS ✨

👑 Mandatory options

• -i, --in=in.bam — input file in BAM format. yes you have to give it. it's the whole point 🫶
• -o, --out=out.bam — output file in BAM format. also required. also the whole point 💖

🌈 Optional options

• -u, --uniq — keep only the best match, remove all matches, if the second best is not much worse
• -q f, --uniqThresh=f — threshold % for uniq, second best must be lower than this fraction of best to keep the best match (default 0.96)
• -b, --best — output all best matches that satisfy minId and minCover
• -e n, --minId=n — minimal percentage of identity (default 92)
• -c n, --minCover=n — minimal percentage of coverage of the query read (default 80)
• -n, --noIntrons — do not allow longer gaps -for RNA-RNA alignments-
• -l n, --insertLimit=n — maximum assumed size of inserts (default 10)
• -s n, --maxSortesTest=n — test if input file is sorted by query name for this number of alignments (default 100000)
• -p, --paired — require that paired reads are on opposite strands of same target. Requires alignment names to contain the suffixes /1,/2 or /f,/r 🧚
• -w, --pairwiseAlignments — use in case alignments were done in pairwise fashion
• -x n, --maxIntronLen=n — maximal separation of paired reads (default 500000)
• -d file, --pairBedFile=file — file name of pairedness coverage: a BED format file in which for each position the number of filtered read pairs is reported that contain the position in or between the reads
• -g file, --commonGeneFile=file — file name in which to write cases where one read maps several different genes
• -t n, --threads=n — use n threads for compression/decompression (default 1); available only if library SeqLib >= 1.2 is used 🔥
• -v, --verbose — output debugging info
• -h, --help — produce help message.

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💜 AUTHORS 💜

AUGUSTUS was written by M. Stanke, O. Keller, S. König, L. Gerischer and L. Romoth. absolute legends, no cap 👑

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📚 ADDITIONAL DOCUMENTATION 📚

An exhaustive documentation can be found in the file /usr/share/doc/augustus/README.md.gz. go read it, bestie, it's giving thorough 📖✨

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ok that's the whole page 🫶 go sort your BAM lexicographically by queryname and slay 💅

FILTERBAM(1) 💖 — that's the source/version tag and it's also on the footer line of the original page, so like, consider it signed, sealed, and delivered by your girl 🌸 mwah 💋